Tutorial: The Siesta Code - PRACE Research … · Main Difference between Siesta and other DFT codes (such as Quantum Espresso): Siesta Was Designed to Scale Linearly with the Number

Tutorial: The Siesta Code

Oswaldo DiéguezDepartment of Materials Science and Engineering

Tel Aviv University7/12/2016

Materials Science Codes on Innovative HPC ArchitecturesPrace-MaX Training

Cineca – Casalecchio di Reno (BO, Italy)5-7 December 2016

Siesta: A Density-Functional Theory Code

Main Difference between Siesta and other DFT codes (such as Quantum Espresso): Siesta Was Designed to Scale Linearly with the Number of Atoms in the Simulation Cell

Implications:● Siesta uses numerical localized atomic orbitals as basis set:

this means that the design of the basis set requires more testing than in the case of plane-wave codes

● *Personal Statement*: Siesta runs faster than any plane-wave code that I have used for the units cells that I have used (between 20 and 120 atoms; the larger the number of atoms, the larger the speed difference)

Today

● How to Get, Install, and Run Siesta● Tutorials (by Javier Junquera)● A Word about Parallelism (by a Non-Expert)

How To Get Siesta

Siesta is Now under the GNU General Public License

How To Get Siesta


How To Get Siesta


How To Get Siesta


How To Get Siesta


How To Get Siesta


How To Get Siesta


How To Get Siesta

Files that you should now have in your computer:

-rwxrwxrwx 1 dieguez dieguez 13132430 Dec 6 09:13 siesta-4.1-b2.tar-rwxrwxrwx 1 dieguez dieguez 989293 Dec 6 09:14 siesta.pdf

How To Get Siesta


tar ball containing all the Siesta files

(source code, documentation, examples, etc)


How To Get Siesta



tar ball containing all the Siesta files

(source code, documentation, examples, etc)

Siesta manual(open it...)

How To Get Siesta

The Siesta Manual

How To Get Siesta

The Siesta Manual

page 8

How To Get Siesta

The Siesta Manual

Pages 8-9

How To Install Siesta: marconi

Transfer the Siesta tar ball to marconi:● this is typically done using a scp utility● for example, from my linux machine, I did: scp /home/dieguez/Downloads/siesta-4.1-b2.tar.gz [email protected]:


Transfer the Siesta tar ball to marconi:● this is typically done using a scp utility● for example, from my linux machine, I did: scp /home/dieguez/Downloads/siesta-4.1-b2.tar.gz [email protected]:

Log in to marconi and check that the tar ball is there:[a08tra74@r000u06l01 ~]$ lssiesta-4.1-b2.tar.gz


Create new directory, move there the tar ball, and uncompress it:

[a08tra74@r000u06l01 ~]$ mkdir SIESTA



[a08tra74@r000u06l01 ~]$ mkdir SIESTA[a08tra74@r000u06l01 ~]$ mv siesta-4.1-b2.tar.gz SIESTA



[a08tra74@r000u06l01 ~]$ mkdir SIESTA[a08tra74@r000u06l01 ~]$ mv siesta-4.1-b2.tar.gz SIESTA[a08tra74@r000u06l01 ~]$ cd SIESTA



[a08tra74@r000u06l01 ~]$ mkdir SIESTA[a08tra74@r000u06l01 ~]$ mv siesta-4.1-b2.tar.gz SIESTA[a08tra74@r000u06l01 ~]$ cd SIESTA[a08tra74@r000u06l01 SIESTA]$ gunzip siesta-4.1-b2.tar.gz



[a08tra74@r000u06l01 ~]$ mkdir SIESTA[a08tra74@r000u06l01 ~]$ mv siesta-4.1-b2.tar.gz SIESTA[a08tra74@r000u06l01 ~]$ cd SIESTA[a08tra74@r000u06l01 SIESTA]$ gunzip siesta-4.1-b2.tar.gz [a08tra74@r000u06l01 SIESTA]$ tar -xvf siesta-4.1-b2.tar



[a08tra74@r000u06l01 ~]$ mkdir SIESTA[a08tra74@r000u06l01 ~]$ mv siesta-4.1-b2.tar.gz SIESTA[a08tra74@r000u06l01 ~]$ cd SIESTA[a08tra74@r000u06l01 SIESTA]$ gunzip siesta-4.1-b2.tar.gz [a08tra74@r000u06l01 SIESTA]$ tar -xvf siesta-4.1-b2.tar[a08tra74@r000u06l01 SIESTA]$ ls -ltotal 46400drwxr-xr-x 10 a08tra74 corsi 4096 Nov 28 10:35 siesta-4.1-b2-rw-r--r-- 1 a08tra74 corsi 47513600 Dec 6 12:09 siesta-4.1-b2.tar


What is in the newly created directory?

[a08tra74@r000u06l01 SIESTA]$ cd siesta-4.1-b2/



[a08tra74@r000u06l01 SIESTA]$ cd siesta-4.1-b2/[a08tra74@r000u06l01 siesta-4.1-b2]$ ls AUTHORS Docs Pseudo Src version.infoCHANGES Examples README TestsCHANGES_DETAILED NOTICE.txt README_TRANSIESTA TutorialsCOPYING Obj RELEASE_NOTES Util



[a08tra74@r000u06l01 SIESTA]$ cd siesta-4.1-b2/[a08tra74@r000u06l01 siesta-4.1-b2]$ ls AUTHORS Docs Pseudo Src version.infoCHANGES Examples README TestsCHANGES_DETAILED NOTICE.txt README_TRANSIESTA TutorialsCOPYING Obj RELEASE_NOTES Util

Version in mid-2014: 269 Fortran-77 files207 Fortran-90 files

15 shell scripts23 m4 files

3 Matlab files1 C file

185,263 lines of code


How to Compile a Serial Executable?(see section 2 of The Siesta Manual)

[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj/



[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj/[a08tra74@r000u06l01 Obj]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)



[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj/[a08tra74@r000u06l01 Obj]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj]$ cp gfortran.make arch.make



[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj/[a08tra74@r000u06l01 Obj]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj]$ cp gfortran.make arch.make[a08tra74@r000u06l01 Obj]$ make[...lots of output messages about the compilation...]



[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj/[a08tra74@r000u06l01 Obj]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj]$ cp gfortran.make arch.make[a08tra74@r000u06l01 Obj]$ make[...lots of output messages about the compilation...][a08tra74@r000u06l01 Obj]$ ls -l siesta-rwxr-xr-x 1 a08tra74 corsi 7298284 Dec 6 15:06 siesta


How to Compile another Serial Executable?

[a08tra74@r000u06l01 Obj]$ cd ..



[a08tra74@r000u06l01 Obj]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_intel/



[a08tra74@r000u06l01 Obj]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_intel/[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj_intel/



[a08tra74@r000u06l01 Obj]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_intel/[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj_intel/[a08tra74@r000u06l01 Obj_intel]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)



[a08tra74@r000u06l01 Obj]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_intel/[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj_intel/[a08tra74@r000u06l01 Obj_intel]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj_intel]$ cp ../Obj/intel.make arch.make



[a08tra74@r000u06l01 Obj]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_intel/[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj_intel/[a08tra74@r000u06l01 Obj_intel]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj_intel]$ cp ../Obj/intel.make arch.make[a08tra74@r000u06l01 Obj_intel]$ module load intel



[a08tra74@r000u06l01 Obj]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_intel/[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj_intel/[a08tra74@r000u06l01 Obj_intel]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj_intel]$ cp ../Obj/intel.make arch.make[a08tra74@r000u06l01 Obj_intel]$ module load intel[a08tra74@r000u06l01 Obj_intel]$ make[...lots of output messages about the compilation...]



[a08tra74@r000u06l01 Obj]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_intel/[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj_intel/[a08tra74@r000u06l01 Obj_intel]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj_intel]$ cp ../Obj/intel.make arch.make[a08tra74@r000u06l01 Obj_intel]$ module load intel[a08tra74@r000u06l01 Obj_intel]$ make[...lots of output messages about the compilation...][a08tra74@r000u06l01 Obj_intel]$ ls -l siesta-rwxr-xr-x 1 a08tra74 corsi 12122531 Dec 6 16:33 siesta


How to Compile a Parallel Executable?

[a08tra74@r000u06l01 Obj_intel]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ mkdir Obj_parallel/[a08tra74@r000u06l01 siesta-4.1-b2]$ cd Obj_parallel/[a08tra74@r000u06l01 Obj_parallel]$ sh ../Src/obj_setup.sh *** Compilation setup done. *** Remember to copy an arch.make file into the directory. *** These files are template arch.make files: *** gfortran.make (for gfortran compiler) *** intel.make (for intel compiler) *** DOCUMENTED-TEMPLATE.make (requires customization)[a08tra74@r000u06l01 Obj_parallel]$ cp ../Obj/DOCUMENTED-TEMPLATE.make arch.make

...and now edit the arch.make to suit marconi...

How To Run Siesta

First, prepare the input files...

[a08tra74@r000u06l01 Obj_intel]$ cd ..[a08tra74@r000u06l01 siesta-4.1-b2]$ cd ..[a08tra74@r000u06l01 SIESTA]$ mkdir h2o/[a08tra74@r000u06l01 SIESTA]$ cd h2o/[a08tra74@r000u06l01 h2o]$ cp ../siesta-4.1-b2/Examples/H2O/h2o.fdf .

How To Run Siesta

[a08tra74@r000u06l01 h2o]$ cat h2o.fdf SystemName Water moleculeSystemLabel h2oNumberOfAtoms 3NumberOfSpecies 2

%block ChemicalSpeciesLabel 1 8 O # Species index, atomic number, species label 2 1 H%endblock ChemicalSpeciesLabel

AtomicCoordinatesFormat Ang%block AtomicCoordinatesAndAtomicSpecies 0.000 0.000 0.000 1 0.757 0.586 0.000 2-0.757 0.586 0.000 2%endblock AtomicCoordinatesAndAtomicSpecies

How To Run Siesta

[a08tra74@r000u06l01 h2o]$ cp ../siesta-4.1-b2/Examples/Vps/O.psf .[a08tra74@r000u06l01 h2o]$ cp ../siesta-4.1-b2/Examples/Vps/H.psf . [a08tra74@r000u06l01 h2o]$ ../siesta-4.1-b2/Obj/siesta < h2o.fdf

Tutorials

● Tutorial 1 (by Javier Junquera): H2O molecule: converging the size of the unit cell for a polar molecule

● Tutorial 2 (by Javier Junquera): Lattice constant, bulk modulus, and equilibrium energy of solids: bulk Si

● Tutorial 3 (by Javier Junquera:Analysis of the charge density in real space of a solid: bulk Si

● Tutorial 4 (by Javier Junquera):Band structure of an ionic solid: the case of MgO

http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Basic/Basic-exercises.html

http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Structuralproperties/Structural.html



A Word About Parallelism in Siesta

[...]

From The Siesta Manual:


From Personal Experience:

Information from: Siesta Tutorial in Zaragoza (2014)

http://departments.icmab.es/leem/siesta/zcam14/Talks/parallelization_talk.pdf


PEXSI Solver:

Information from: Siesta Tutorial in Zaragoza (2014)

http://departments.icmab.es/leem/siesta/zcam14/Talks/parallelization_talk.pdf


More About Siesta

● Tutorials: webpages of Javier Junquera● Documentation (tutorials, manuals, videos): old Siesta page ● About the method: Technical Publications● Getting Siesta and collaborating: Launchpad● Asking questions: Siesta Mailing List

[email protected]

http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Hands-on-session.html

http://departments.icmab.es/leem/siesta/Documentation/index.html

http://departments.icmab.es/leem/siesta/Documentation/Publications/basic_pubs.html

https://launchpad.net/siesta/

http://departments.icmab.es/leem/siesta/Documentation/list.html

Documents

Tutorial: The Siesta Code - PRACE Research … · Main Difference between Siesta and other DFT codes (such as Quantum Espresso): Siesta Was Designed to Scale Linearly with the Number